SARS-CoV-2 3CLPro in complex with 2-(benzotriazol-1-yl)-N-[4-(1H-pyrazol-4-yl)phenyl]-N-(3-thienylmethyl)acetamide

Experimental Data Snapshot

  • Resolution: 1.96 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 

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Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


Structure-Based Optimization of ML300-Derived, Noncovalent Inhibitors Targeting the Severe Acute Respiratory Syndrome Coronavirus 3CL Protease (SARS-CoV-2 3CL pro ).

Han, S.H.Goins, C.M.Arya, T.Shin, W.J.Maw, J.Hooper, A.Sonawane, D.P.Porter, M.R.Bannister, B.E.Crouch, R.D.Lindsey, A.A.Lakatos, G.Martinez, S.R.Alvarado, J.Akers, W.S.Wang, N.S.Jung, J.U.Macdonald, J.D.Stauffer, S.R.

(2022) J Med Chem 65: 2880-2904

  • DOI: https://doi.org/10.1021/acs.jmedchem.1c00598
  • Primary Citation of Related Structures:  
    7LMD, 7LME, 7LMF, 7LMG, 7LMH, 7LMI, 7LMJ

  • PubMed Abstract: 

    Starting from the MLPCN probe compound ML300, a structure-based optimization campaign was initiated against the recent severe acute respiratory syndrome coronavirus (SARS-CoV-2) main protease (3CL pro ). X-ray structures of SARS-CoV-1 and SARS-CoV-2 3CL pro enzymes in complex with multiple ML300-based inhibitors, including the original probe ML300, were obtained and proved instrumental in guiding chemistry toward probe compound 41 (CCF0058981). The disclosed inhibitors utilize a noncovalent mode of action and complex in a noncanonical binding mode not observed by peptidic 3CL pro inhibitors. In vitro DMPK profiling highlights key areas where further optimization in the series is required to obtain useful in vivo probes. Antiviral activity was established using a SARS-CoV-2-infected Vero E6 cell viability assay and a plaque formation assay. Compound 41 demonstrates nanomolar activity in these respective assays, comparable in potency to remdesivir. These findings have implications for antiviral development to combat current and future SARS-like zoonotic coronavirus outbreaks.

  • Organizational Affiliation

    Center for Therapeutics Discovery, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C-like proteinase306Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
EC: (PDB Primary Data), (UniProt), 3.4.22 (UniProt), (UniProt), (UniProt), (UniProt), 3.1.13 (UniProt), 4.6.1 (UniProt), (UniProt)
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTD1 
Go to UniProtKB:  P0DTD1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTD1
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Y6A (Subject of Investigation/LOI)
Query on Y6A

Download Ideal Coordinates CCD File 
B [auth A]2-(benzotriazol-1-yl)-~{N}-[4-(1~{H}-pyrazol-4-yl)phenyl]-~{N}-(thiophen-3-ylmethyl)ethanamide
C22 H18 N6 O S
Experimental Data & Validation

Experimental Data

  • Resolution: 1.96 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.159α = 90
b = 54.341β = 101.01
c = 44.45γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-11
    Type: Initial release
  • Version 1.1: 2021-08-25
    Changes: Database references
  • Version 1.2: 2022-03-09
    Changes: Database references
  • Version 1.3: 2023-10-18
    Changes: Data collection, Refinement description